Load prepared data

prepared_data <- read.table("../data/features.tsv", sep = "\t", header=TRUE)
totalTable <- NULL
totalTable$sd <- prepared_data$sd
totalTable$mean <- prepared_data$mean
totalTableOfMeans <- NULL
totalTableOfMeans$sd <- prepared_data$MeansSD
y <- NULL
y$Means <- prepared_data$res
ylog <- NULL
ylog$Means <- prepared_data$logres

Graphics of dependencies of result on different features

library(lattice)

xyplot(ylog$Means ~ prepared_data$Amplicon_GC_content,  xlab="GC-content(%)", ylab="log of amplicon percental amount", main="Amplicon GC-content")

xyplot(ylog$Means ~ prepared_data$Amplicon_Len,  xlab="Length", ylab="log of amplicon percental amount", main="Amplicon length")

xyplot(ylog$Means ~ prepared_data$Fwd_Primer_GC_content,  xlab="GC-content(%)", ylab="log of amplicon percental amount", main="Forward Primer GC-content")

xyplot(ylog$Means ~ prepared_data$Fwd_Primer_Len,  xlab="Length", ylab="log of amplicon percental amount", main="Forward Primer length")

xyplot(ylog$Means ~ prepared_data$Rev_Primer_GC_content,  xlab="GC-content(%)", ylab="log of amplicon percental amount", main="Reverse Primer GC-content")

xyplot(ylog$Means ~ prepared_data$Rev_Primer_Len,  xlab="Length", ylab="log of amplicon percental amount", main="Reverse Primer length")

xyplot(y$Means ~ prepared_data$Amplicon_GC_content,  xlab="GC-content(%)", ylab="amplicon percental amount", main="Amplicon GC-content")

xyplot(y$Means ~ prepared_data$Amplicon_Len,  xlab="Length", ylab="amplicon percental amount", main="Amplicon length")

xyplot(y$Means ~ prepared_data$Fwd_Primer_GC_content,  xlab="GC-content(%)", ylab="amplicon percental amount", main="Forward Primer GC-content")

xyplot(y$Means ~ prepared_data$Fwd_Primer_Len,  xlab="Length", ylab="amplicon percental amount", main="Forward Primer length")

xyplot(y$Means ~ prepared_data$Rev_Primer_GC_content,  xlab="GC-content(%)", ylab="amplicon percental amount", main="Reverse Primer GC-content")

xyplot(y$Means ~ prepared_data$Rev_Primer_Len,  xlab="Length", ylab="amplicon percental amount", main="Reverse Primer length")

xyplot(totalTable$mean ~ prepared_data$Amplicon_GC_content,  xlab="GC-content(%)", ylab="mean of amplicon percental amount", main="Amplicon GC-content")

xyplot(totalTable$mean ~ prepared_data$Amplicon_Len,  xlab="Length", ylab="mean of amplicon percental amount", main="Amplicon length")

xyplot(totalTable$mean ~ prepared_data$Fwd_Primer_GC_content,  xlab="GC-content(%)", ylab="mean of amplicon percental amount", main="Forward Primer GC-content")

xyplot(totalTable$mean ~ prepared_data$Fwd_Primer_Len,  xlab="Length", ylab="mean of amplicon percental amount", main="Forward Primer length")

xyplot(totalTable$mean ~ prepared_data$Rev_Primer_GC_content,  xlab="GC-content(%)", ylab="mean of  amplicon percental amount", main="Reverse Primer GC-content")

xyplot(totalTable$mean ~ prepared_data$Rev_Primer_Len,  xlab="Length", ylab="mean of amplicon percental amount", main="Reverse Primer length")

xyplot(totalTable$sd ~ prepared_data$Amplicon_GC_content,  xlab="GC-content(%)", ylab="sd of amplicon percental amount", main="Amplicon GC-content")

xyplot(totalTable$sd ~ prepared_data$Amplicon_Len,  xlab="Length", ylab="sd of amplicon percental amount", main="Amplicon length")

xyplot(totalTable$sd ~ prepared_data$Fwd_Primer_GC_content,  xlab="GC-content(%)", ylab="sd of amplicon percental amount", main="Forward Primer GC-content")

xyplot(totalTable$sd ~ prepared_data$Fwd_Primer_Len,  xlab="Length", ylab="sd of amplicon percental amount", main="Forward Primer length")

xyplot(totalTable$sd ~ prepared_data$Rev_Primer_GC_content,  xlab="GC-content(%)", ylab="sd of  amplicon percental amount", main="Reverse Primer GC-content")

xyplot(totalTable$sd ~ prepared_data$Rev_Primer_Len,  xlab="Length", ylab="sd of amplicon percental amount", main="Reverse Primer length")

xyplot(log(totalTable$mean) ~ prepared_data$Amplicon_GC_content,  xlab="GC-content(%)", ylab="mean of amplicon percental amount", main="Amplicon GC-content")

xyplot(log(totalTable$mean) ~ prepared_data$Amplicon_Len,  xlab="Length", ylab="mean of amplicon percental amount", main="Amplicon length")

xyplot(log(totalTable$mean) ~ prepared_data$Fwd_Primer_GC_content,  xlab="GC-content(%)", ylab="mean of amplicon percental amount", main="Forward Primer GC-content")

xyplot(log(totalTable$mean) ~ prepared_data$Fwd_Primer_Len,  xlab="Length", ylab="mean of amplicon percental amount", main="Forward Primer length")

xyplot(log(totalTable$mean) ~ prepared_data$Rev_Primer_GC_content,  xlab="GC-content(%)", ylab="mean of  amplicon percental amount", main="Reverse Primer GC-content")

xyplot(log(totalTable$mean) ~ prepared_data$Rev_Primer_Len,  xlab="Length", ylab="mean of amplicon percental amount", main="Reverse Primer length")

2. MaxPolyX

xyplot(totalTable$mean ~ prepared_data$Fwd_Primer_MaxPolyX,  xlab="MaxPolyX", ylab="mean of amplicon percental amount", main="Forward Primer")

xyplot(totalTable$mean ~ prepared_data$Rev_Primer_MaxPolyX,  xlab="MaxPolyX", ylab="mean of amplicon percental amount", main="Reverse Primer")

xyplot(totalTable$mean ~ prepared_data$Amplicon_MaxPolyX,  xlab="MaxPolyX", ylab="mean of amplicon percental amount", main="Amplicon")

xyplot(totalTable$sd ~ prepared_data$Fwd_Primer_MaxPolyX,  xlab="MaxPolyX", ylab="sd of amplicon percental amount", main="Forward Primer")

xyplot(totalTable$sd ~ prepared_data$Rev_Primer_MaxPolyX,  xlab="MaxPolyX", ylab="sd of amplicon percental amount", main="Reverse Primer")

xyplot(totalTable$sd ~ prepared_data$Amplicon_MaxPolyX,  xlab="MaxPolyX", ylab="sd of amplicon percental amount", main="Amplicon")

2. Entropy

xyplot(totalTable$mean ~ prepared_data$Fwd_Primer_Entropy,  xlab="Entropy", ylab="mean of amplicon percental amount", main="Forward Primer")

xyplot(totalTable$mean ~ prepared_data$Rev_Primer_Entropy,  xlab="Entropy", ylab="mean of amplicon percental amount", main="Reverse Primer")

xyplot(totalTable$mean ~ prepared_data$Amplicon_Entropy,  xlab="Entropy", ylab="mean of amplicon percental amount", main="Amplicon")

xyplot(totalTable$sd ~ prepared_data$Fwd_Primer_Entropy,  xlab="Entropy", ylab="sd of amplicon percental amount", main="Forward Primer")

xyplot(totalTable$sd ~ prepared_data$Rev_Primer_Entropy,  xlab="Entropy", ylab="sd of amplicon percental amount", main="Reverse Primer")

xyplot(totalTable$sd ~ prepared_data$Amplicon_Entropy,  xlab="Entropy", ylab="sd of amplicon percental amount", main="Amplicon")

2. Hash

xyplot(totalTable$mean ~ prepared_data$Fwd_Primer_Hash,  xlab="Hash", ylab="mean of amplicon percental amount", main="Forward Primer")

xyplot(totalTable$mean ~ prepared_data$Rev_Primer_Hash,  xlab="Hash", ylab="mean of amplicon percental amount", main="Reverse Primer")

xyplot(totalTable$mean ~ prepared_data$Amplicon_Hash,  xlab="Hash", ylab="mean of amplicon percental amount", main="Amplicon")

xyplot(totalTable$sd ~ prepared_data$Fwd_Primer_Hash,  xlab="Hash", ylab="sd of amplicon percental amount", main="Forward Primer")

xyplot(totalTable$sd ~ prepared_data$Rev_Primer_Hash,  xlab="Hash", ylab="sd of amplicon percental amount", main="Reverse Primer")

xyplot(totalTable$sd ~ prepared_data$Amplicon_Hash,  xlab="Hash", ylab="sd of amplicon percental amount", main="Amplicon")

Graphics of dependencies of standard variation of result

bwplot(prepared_data$Fwd_END_3 ~ ylog$Means,     ylab="nucleotids", xlab="log of amplicon percental amount", 
       main="Forward primer 3' end")

bwplot(prepared_data$Rev_END_3 ~ ylog$Means,     ylab="nucleotids", xlab="log of amplicon percental amount", 
       main="Reverse primer 3' end")

bwplot(prepared_data$Start_Dangling_End ~ ylog$Means,     ylab="nucleotids", xlab="log of amplicon percental amount", 
       main="First dangling end")

bwplot(prepared_data$Stop_Dangling_End ~ ylog$Means,     ylab="nucleotids", xlab="log of amplicon percental amount", 
       main="Second dangling end")

bwplot(prepared_data$Fwd_END_3 ~ y$Means,     ylab="nucleotids", xlab="amplicon percental amount", 
        main="Forward primer 3' end")

bwplot(prepared_data$Rev_END_3 ~ y$Means,     ylab="nucleotids", xlab="amplicon percental amount", 
        main="Reverse primer 3' end")

bwplot(prepared_data$Start_Dangling_End ~ y$Means,     ylab="nucleotids", xlab="amplicon percental amount", 
      main="First dangling end")

bwplot(prepared_data$Stop_Dangling_End ~ y$Means,     ylab="nucleotids", xlab="amplicon percental amount", 
       main="Second dangling end")

bwplot(prepared_data$Fwd_END_3 ~ totalTable$sd,     ylab="nucleotids", xlab="standard deviation of amplicon percental amount", 
        main="Forward primer 3' end")

bwplot(prepared_data$Rev_END_3 ~ totalTable$sd,     ylab="nucleotids", xlab="standard deviation of amplicon percental amount", 
        main="Reverse primer 3' end")

bwplot(prepared_data$Start_Dangling_End ~ totalTable$sd,     ylab="nucleotids", xlab="standard deviation of amplicon percental amount", 
      main="First dangling end")

bwplot(prepared_data$Stop_Dangling_End ~ totalTable$sd,     ylab="nucleotids", xlab="standard deviation of amplicon percental amount", 
       main="Second dangling end")

bwplot(prepared_data$Fwd_END_3 ~ totalTable$mean,     ylab="nucleotids", xlab="mean of amplicon percental amount", 
        main="Forward primer 3' end")

bwplot(prepared_data$Rev_END_3 ~ totalTable$mean,     ylab="nucleotids", xlab="mean of amplicon percental amount", 
        main="Reverse primer 3' end")

bwplot(prepared_data$Start_Dangling_End ~ totalTable$mean,     ylab="nucleotids", xlab="mean of amplicon percental amount", 
      main="First dangling end")

bwplot(prepared_data$Stop_Dangling_End ~ totalTable$mean,     ylab="nucleotids", xlab="mean of amplicon percental amount", 
       main="Second dangling end")

amplicon_len <- prepared_data$Amplicon_Len
q <- quantile(amplicon_len, probs = c(1/4, 1/2, 3/4, 1))
amplicon_len[amplicon_len <= q[1]] <- q[1]
amplicon_len[amplicon_len > q[1] & amplicon_len <= q[2]] <- q[2]
amplicon_len[amplicon_len > q[2] & amplicon_len <= q[3]] <- q[3]
amplicon_len[amplicon_len > q[3]] <- q[4]
histogram(amplicon_len)

bwplot(amplicon_len ~ y$Means,     ylab="length", xlab="amplicon percental amount", 
       main="Amplicon length")

bwplot(amplicon_len ~ ylog$Means,     ylab="length", xlab="log of amplicon percental amount", 
       main="Amplicon length")

bwplot(amplicon_len ~ totalTable$sd,     ylab="length",  xlab="standard deviation of amplicon percental amount", 
       main="Amplicon length")

bwplot(amplicon_len ~ totalTable$mean,     ylab="length",  xlab="mean of amplicon percental amount", 
       main="Amplicon length")

amplicon_gc <- prepared_data$Amplicon_GC_content
q <- quantile(amplicon_gc, probs = c(1/4, 1/2, 3/4, 1))
amplicon_gc[amplicon_gc <= q[1]] <- q[1]
amplicon_gc[amplicon_gc > q[1] & amplicon_gc <= q[2]] <- q[2]
amplicon_gc[amplicon_gc > q[2] & amplicon_gc <= q[3]] <- q[3]
amplicon_gc[amplicon_gc > q[3]] <- q[4]
histogram(amplicon_gc)

bwplot(amplicon_gc ~ y$Means,     ylab="GC-content", xlab="amplicon percental amount", 
       main="Amplicon GC-content")

bwplot(amplicon_gc ~ ylog$Means,   ylab="GC-content", xlab="log of amplicon percental amount", 
       main="Amplicon GC-content")

bwplot(amplicon_gc ~ totalTable$sd,  ylab="GC-content",  xlab="standard deviation of amplicon percental amount", 
       main="Amplicon GC-content")

bwplot(amplicon_gc ~ totalTable$mean,  ylab="GC-content",  xlab="mean of amplicon percental amount", 
       main="Amplicon GC-content")

primer_len <- prepared_data$Fwd_Primer_Len
q <- quantile(primer_len, probs = c(1/4, 1/2, 3/4, 1))
primer_len[primer_len <= q[1]] <- q[1]
primer_len[primer_len > q[1] & primer_len <= q[2]] <- q[2]
primer_len[primer_len > q[2] & primer_len <= q[3]] <- q[3]
primer_len[primer_len > q[3]] <- q[4]
histogram(primer_len)

bwplot(primer_len ~ y$Means,     ylab="length", xlab="primer percental amount", 
       main="Forward Primer length")

bwplot(primer_len ~ ylog$Means,   ylab="length", xlab="log of amplicon percental amount", 
       main="Forward Primer length")

bwplot(primer_len ~ totalTable$sd,  ylab="length",  xlab="standard deviation of amplicon percental amount", 
       main="Forward Primer length")

bwplot(primer_len ~ totalTable$mean,  ylab="length",  xlab="mean of amplicon percental amount", 
       main="Forward Primer length")

primer_gc <- prepared_data$Fwd_Primer_GC_content
q <- quantile(primer_gc, probs = c(1/4, 1/2, 3/4, 1))
primer_gc[primer_gc <= q[1]] <- q[1]
primer_gc[primer_gc > q[1] & primer_gc <= q[2]] <- q[2]
primer_gc[primer_gc > q[2] & primer_gc <= q[3]] <- q[3]
primer_gc[primer_gc > q[3]] <- q[4]
bwplot(primer_gc ~ y$Means,     ylab="GC-content", xlab="primer percental amount", 
       main="Forward Primer GC-content")

bwplot(primer_gc ~ ylog$Means,   ylab="GC-content", xlab="log of amplicon percental amount", 
       main="Forward Primer GC-content")

bwplot(primer_gc ~ totalTable$sd,  ylab="GC-content",  xlab="standard deviation of amplicon percental amount", 
       main="Forward Primer GC-content")

bwplot(primer_gc ~ totalTable$mean,  ylab="GC-content",  xlab="mean of amplicon percental amount", 
       main="Forward Primer GC-content")

primer_len <- prepared_data$Rev_Primer_Len
q <- quantile(primer_len, probs = c(1/4, 1/2, 3/4, 1))
primer_len[primer_len <= q[1]] <- q[1]
primer_len[primer_len > q[1] & primer_len <= q[2]] <- q[2]
primer_len[primer_len > q[2] & primer_len <= q[3]] <- q[3]
primer_len[primer_len > q[3]] <- q[4]
histogram(primer_len)

bwplot(primer_len ~ y$Means,     ylab="length", xlab="primer percental amount", 
       main="Reverse Primer length")

bwplot(primer_len ~ ylog$Means,   ylab="length", xlab="log of amplicon percental amount", 
       main="Reverse Primer length")

bwplot(primer_len ~ totalTable$sd,  ylab="length",  xlab="standard deviation of amplicon percental amount", 
       main="Reverse Primer length")

bwplot(primer_len ~ totalTable$mean,  ylab="length",  xlab="mean of amplicon percental amount", 
       main="Reverse Primer length")

primer_gc <- prepared_data$Rev_Primer_GC_content
q <- quantile(primer_gc, probs = c(1/4, 1/2, 3/4, 1))
primer_gc[primer_gc <= q[1]] <- q[1]
primer_gc[primer_gc > q[1] & primer_gc <= q[2]] <- q[2]
primer_gc[primer_gc > q[2] & primer_gc <= q[3]] <- q[3]
primer_gc[primer_gc > q[3]] <- q[4]
bwplot(primer_gc ~ y$Means,     ylab="GC-content", xlab="primer percental amount", 
       main="Reverse Primer GC-content")

bwplot(primer_gc ~ ylog$Means,   ylab="GC-content", xlab="log of amplicon percental amount", 
       main="Reverse Primer GC-content")

bwplot(primer_gc ~ totalTable$sd,  ylab="GC-content",  xlab="standard deviation of amplicon percental amount", 
       main="Reverse Primer GC-content")

bwplot(primer_gc ~ totalTable$mean,  ylab="GC-content",  xlab="mean of amplicon percental amount", 
       main="Reverse Primer GC-content")